I'm not sure I understand boss, but it doesnt sound like what you have will make your car run.
A stock PCM needs more harness than what you are describing that the fast harness has.
I saw no crank/cam senor mentioned
CTS
TPS
MAF
ETC
ETC
ETC
also without the wiring harness for the 4L60E you have nothing to run it. You will now need a stand alone controller and wiring to run the trans.
What you should do, is go to the salvage yard and get a complete powertrain harness from a 2001 LS1 car and use the stock PCM you have and run it.
Then get a complete wiring diagram for the LS1 on paper and tape it to the windshield,Plug in everything that plugs in,and then look at the power and ground circuits, and wire them in accordingly.
There is no "Magic Harness" out there that will just plug and play for your car.
The best, and most cost effective way to do a conversion of your type is to get the OE harness, and fab it up nice and neat into your ride.
Trust me you will need to bone up on doing the wiring to get it to turn out right,in the end you will like it.
If you retain the OBD II diagnostic connector, that is a big plus, as you can change the tune with a laptop, a few cables and a program .
Keeping it fully intact will keep you 50 state legal, will be easier to diagnose, and is tuneable for more fun. Not to mention those guys at the chevy dealer will drool when they look under the hood.
Honestly, it is by far cheaper and better to hybridize a factory harness into your ride.For me it would be a piece of cake and a pleasure.
Plenty of help here, just get your mind made up after studying the problem at hand and go for it.I am sure we can come up with something.
If you can post a wiring diagram of the harness you have I would be interested to see it, just to clarify whether or not it even has any use in your build.